http://aero.go.usu.edu/ MachUp and CloudFoil software (web interface) specialized for design of airframes and foils. You can design and analyze flying machines, drones, model aircraft and other aerodynamic objects. There is a free and Pro version.

Programmatic CAD

OpenSCAD OpenSCAD is a software for creating solid 3D CAD models. It is free software and available for Linux/UNIX, Windows and Mac OS X. Unlike most free software for creating 3D models (such as Blender) it does not focus on the artistic aspects of 3D modeling but instead on the CAD aspects. Basically: it means that you will have to write code, learn a lot and you will need some time if you are a beginner.

http://www.reprap.org/wiki/Kamaq Kamaq RepRap firmware which is Linux based and written in Python. It has a web-interface in HTML5/JavaScript and websockets. It controls up to 4 stepper motors (axes) via standard USB audio device, end-switches, and heaters via GPIO and hw-mon.

GCMC http://www.vagrearg.org/content/gcmc-intro G-code generator. It is a front-end language aimed at producing human-readable machine routines. By abstracting away the unnecessary idiosyncrasies of the language, GCMC enables you to generate complex tool movements and patterns.

http://sourceforge.net/projects/dxf2gcode/ dxf2gcode G-code generator. Makes gcode based on an original DXF design file that also features automatic cutter compensation done in software. It is a very useful feature that will generate an offset tool-path based on the diameter of the tool and the type of cut (pocket or outside edge).

https://www.botqueue.com/ BotQueue lets you control multiple 3D printers through the Internet and turn them into your own manufacturing center. Think cloud-based computing, but for making things in the real world. Now you can build the robot army you've always dreamed of! Oh yeah, and it's 100% open source.

3D Printing and digital fabrication business software

http://makeros.com/ maker OS is a web based application for running an digital fabrication small business.

http://www.printocracy.io/ Printocracy is an online quotation generator for you 3d printing business. You can set up many parameters and generate price quotations via a widget on your website.

http://printelize.com/en/ Printelize is an online sales automation software designed for businesses that provide 3D printing services.

CNC Software

http://camotics.org/ CAMotics is an Open-Source software which simulates 3-axis CNC milling or engraving. It is a fast, flexible and user friendly simulation software for the DIY and Open-Source community. CAMotics works on Linux, OS-X and Windows.

Geography, mapping and 3d printing

http://jthatch.com/Moon2STL/ Generate 3d printable .stl files based on Moon map data. Moon2STL uses data from the Unified Lunar Control Network 2005, a topographical model of the lunar surface, provided online by the US Geological Survey. Made from a network of photos derived from Earth-based and Apollo photographs, as well as Mariner 10 and Galileo images.

http://osmbuildings.org/ Open Street Map Buildings, is an open source map with 3d models of buildings. You can download .stl files from the menu.

Various other software

http://meshlab.sourceforge.net/ MeshLab is an open source, portable, and extensible system for the processing and editing of unstructured 3D triangular meshes. The system is aimed to help the processing of the typical not-so-small unstructured models arising in 3D scanning, providing a set of tools for editing, cleaning, healing, inspecting, rendering and converting this kind of meshes.

http://abfab3d.com AbFab3D is a toolkit to help in the development of 3D printing tools and editors. The toolkit will contain both Voxel and Triangle aware code and will include functions for changing between them. The goal is to make creating 3D editors easier.

http://slicer.org/Slicer is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X.

http://www.greentoken.de/onlineconv/ Online 3D Model Converter, online web application that is a tool to convert digital 3d model files from one file format to another (ie.: FBX to OBJ or OBJ to STL for 3D printing, DAE to JSON for use with WebGL, ..).

Software libraries, frameworks etc.:

http://jreinhardt.github.io/BOLTS/index.html The aim of BOLTS is to build a free and open-source standard parts library for CAD applications. It does so by providing a common database that can be utilized by many different CAD applications.

http://pygestalt.org/ Gestalt is a framework for building controllers for automated tools. It enables you to import your machines as Python modules, and makes it easy to connect machines to browser-based user interfaces. Gestalt will be available as an open source library in November 2013.
In the interim, you can read about Gestalt in much more detail here.

http://pypy.org/ PyPy is faster and compliant implementation of Python language. Useful to speed up slicing 3D Models using skeinforge.py or other Python applications.

http://www.osteo3d.com/ Osteo3D has the ability to create 3d models from medical scan files and has a repository of medical models with ability to create custom 3d printed guides for medical procedures